Learning Documentation CommunityOpen ExchangeGlobal Masters Certification Partner Directory Ideas Portal

Submit application

iris-r-gateway-template

Downloads9

Bookmark

This application is not supported by InterSystems Corporation. Please be notified that you use it at your own responsibility.

Details

Releases

Reviews

Issues

What's new in this version

Initial Release

iris-r-gateway-template

This repository is a template for using the new R gateway for IRIS 2021.1.

The architecture of this template is as follows:

It is composed of three containers, with one for:

IRIS
R and RServe
A Java Gateway

Iris and the R server will discuss through the java gateway.

These first two containers are bound to the data/ local folder, and so have access to the same data:

abalone.csv

This file is loaded as a table in IRIS :

Test.Data

The R container also has access to the r/ folder, and in it is the following script:

test.R

getMode <- function(x) {
  l <- unique(x)
  l[which.max(tabulate(match(x, l)))]
}
getLength <- function(x) {

length(x)

}
createHistJPG <- function(data, dir, label) {

dir2 = paste(dir, "/hist.jpeg", sep="")

jpeg(file = dir2)

hist(data, xlab=label)

dev.off()

}
createHistPNG <- function(data, dir, label) {

dir2 = paste(dir, "/hist.png", sep="")

png(file = dir2)

hist(data, xlab=label)

dev.off()

}
createHistPDF <- function(data, dir, label) {

dir2 = paste(dir, "/hist.pdf", sep="")

pdf(file = dir2)

hist(data, xlab=label)

dev.off()

}

Run this template

git clone https://github.com/grongierisc/iris-r-gateway-template

then :

docker compose up

Play with this template

Run the following ObjectScript commands

Run random R expression

do ##class(Demo.RGateway).RunEval()

output :

"R version 3.4.4 (2018-03-15)"

code :

ClassMethod RunEval() As %Status
{
	// Get a gateway instance
    set gateway = ##class(%Net.Remote.Gateway).%New()
    set tSC = gateway.%Connect(..#JGWHOST, ..#JGWPORT)
	if $$$ISERR(tSC) quit
	// Bind the gateway to the Rserve

set c = ##class(%Net.Remote.Object).%ClassMethod(.gateway,"com.intersystems.rgateway.Helper","createRConnection", ..#RHOST, ..#RPORT)
	// Run a random R command

zw c.eval("R.version$version.string").asString()
<span class="pl-k">do</span>:<span class="pl-v">c</span>'=<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> <span class="pl-v">c</span>.<span class="pl-e">close</span>()
<span class="pl-k">do</span>:<span class="pl-v">gateway</span>'=<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> <span class="pl-v">gateway</span>.<span class="pl-e">%Disconnect</span>()
<span class="pl-k">quit</span>

}

Run R expression from IRIS SQL

do ##class(Demo.RGateway).FromSQLOnIris()

output :

"mean = 0.5239920995930093"
"median = 0.545"

code :

ClassMethod FromSQLOnIris()
{
    set gateway = ##class(%Net.Remote.Gateway).%New()
    set tSC = gateway.%Connect("r",55554)
	if $$$ISERR(tSC) quit
<span class="pl-k">set</span> <span class="pl-v">c</span> = <span class="pl-k">##class</span>(<span class="pl-en">%Net.Remote.Object</span>).<span class="pl-e">%ClassMethod</span>(.<span class="pl-e">gateway</span>,<span class="pl-s"><span class="pl-pds">"</span>com.intersystems.rgateway.Helper<span class="pl-pds">"</span></span>,<span class="pl-s"><span class="pl-pds">"</span>createRConnection<span class="pl-pds">"</span></span>)

	// SQL Query

set q = "select length from Test.Data"

set resultSet = ##class(%SQL.Statement).%ExecDirect( , .q)
	// Prepare R vector

do c.eval("l = c()")

while resultSet.%Next() {

		 // Append resultSet to the R vector

do c.assign("x", ##class(%Net.Remote.Object).%New(gateway, "org.rosuda.REngine.REXPDouble", resultSet.Length))

do c.eval("l = append(l, c(x))")

}
	// Produce mean from R

zw "mean = " _c.eval("mean(l)").asString()
	// Produce median from R

zw "median = "_c.eval("median(l)").asString()
<span class="pl-k">do</span>:<span class="pl-v">c</span>'=<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> <span class="pl-v">c</span>.<span class="pl-e">close</span>()
<span class="pl-k">do</span>:<span class="pl-v">gateway</span>'=<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> <span class="pl-v">gateway</span>.<span class="pl-e">%Disconnect</span>()
<span class="pl-k">quit</span>

}

Run R Script and plot

do ##class(Demo.RGateway).FromCSVOnRServe()

output :

"mean = 0.5239920995930093"
"median = 0.545"
"mode = 0.55"
"plot produced in /tmp/data/hist.png"
"plot produced in /tmp/data/hist.jpeg"
"plot produced in /tmp/data/hist.pdf"

code :

ClassMethod FromCSVOnRServe()
{
    set gateway = ##class(%Net.Remote.Gateway).%New()
    set tSC = gateway.%Connect(..#JGWHOST, ..#JGWPORT)
	if $$$ISERR(tSC) quit
<span class="pl-k">set</span> <span class="pl-v">c</span> = <span class="pl-k">##class</span>(<span class="pl-en">%Net.Remote.Object</span>).<span class="pl-e">%ClassMethod</span>(.<span class="pl-e">gateway</span>,<span class="pl-s"><span class="pl-pds">"</span>com.intersystems.rgateway.Helper<span class="pl-pds">"</span></span>,<span class="pl-s"><span class="pl-pds">"</span>createRConnection<span class="pl-pds">"</span></span>, ..#RHOST, ..#RPORT)

	// Read a file from R

	// assign an R variable for the data file 

set filename = "/tmp/data/abalone.csv"

do c.assign("filename", filename)

	// Read the file from the R server

do c.eval("data = read.csv(filename)")
<span class="pl-k">zw</span> <span class="pl-s"><span class="pl-pds">"</span>mean = <span class="pl-pds">"</span></span>_<span class="pl-v">c</span>.<span class="pl-e">eval</span>(<span class="pl-s"><span class="pl-pds">"</span>mean(data$Length)<span class="pl-pds">"</span></span>).<span class="pl-e">asString</span>()
<span class="pl-k">zw</span> <span class="pl-s"><span class="pl-pds">"</span>median = <span class="pl-pds">"</span></span>_<span class="pl-v">c</span>.<span class="pl-e">eval</span>(<span class="pl-s"><span class="pl-pds">"</span>median(data$Length)<span class="pl-pds">"</span></span>).<span class="pl-e">asString</span>()

	// Call function from R script

	// assign an R variable for the script file 

do c.assign("rFile", "/tmp/r/src/test.R")

do c.eval("source(rFile)")
<span class="pl-k">zw</span> <span class="pl-s"><span class="pl-pds">"</span>mode = <span class="pl-pds">"</span></span>_<span class="pl-v">c</span>.<span class="pl-e">eval</span>(<span class="pl-s"><span class="pl-pds">"</span>getMode(data$Length)<span class="pl-pds">"</span></span>).<span class="pl-e">asString</span>()

	// Plot graphs

	// assign a directory to save files

do c.assign("dir", "/tmp/data")

	// produce plot PNG

do c.eval("createHistPNG(data$Rings, dir, ""Rings"")")

zw "plot produced in /tmp/data/hist.png"

	// produce plot JPG

do c.eval("createHistJPG(data$Rings, dir, ""Rings"")")

zw "plot produced in /tmp/data/hist.jpeg"

	// produce plot PDF

do c.eval("createHistPDF(data$Rings, dir, ""Rings"")")

zw "plot produced in /tmp/data/hist.pdf"
<span class="pl-k">do</span>:<span class="pl-v">c</span>'=<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> <span class="pl-v">c</span>.<span class="pl-e">close</span>()
<span class="pl-k">do</span>:<span class="pl-v">gateway</span>'=<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> <span class="pl-v">gateway</span>.<span class="pl-e">%Disconnect</span>()
<span class="pl-k">quit</span>

}

Another R Gateway

You can have a look at this R Gateway for IRIS :

https://github.com/intersystems-community/RGateway

This one doesn't use the java gateway and use a direct connection between IRIS and R Server.

Exemple :

Set c = ##class(R.RConnection).%New() // Create a R client
Set x = ##class(R.REXPDouble).%New(3.0) // A single double value
Do c.assign("x", x) // Assign the value to R variable x
Do c.eval("y<-sqrt(x)") // Evaluate R script
Set y = c.get("y") // Get the value of R variable y
Write y.toJSON().%ToJSON()

Rating

(1)

iris-r-gateway-template

What's new in this version

iris-r-gateway-template

Run this template

Play with this template

Run random R expression

Run R expression from IRIS SQL

Run R Script and plot

Another R Gateway

Tag version: 1.0.0

Released: 2021-06-17 13:56:41